def test_PointSoucePotential_00(self):
'''test PointSourcePotential implementation'''
cell = get_cell(n_seg=3)
sigma = 0.3
r = np.array([[29.41099547, 43.06748789, -13.90864482, -40.44348899,
-29.4355596, -49.53871099, -33.70179906, 19.71508449,
-25.38725944, 42.52608652],
[24.36798674, -31.25870899, 22.6071361, -5.89078286,
44.44040172, 48.8092616, -34.2306679, -12.08847587,
-30.36317994, 30.79944143],
[-33.67242089, -9.71721014, 22.74564354, -27.14076556,
10.26397085, 30.1274518, -36.71772572, -22.21636375,
35.62274778, 41.273182]])
psp = lfp.PointSourcePotential(cell=cell, x=r[0], y=r[1, ], z=r[2, ],
sigma=sigma)
M = psp.get_transformation_matrix()
imem = np.array([[-1., 1.],
[0., 0.],
[1., -1.]])
V_ex = M @ imem
r_norm = np.empty((r.shape[1], cell.totnsegs))
for i, (x, y, z) in enumerate(zip(cell.x.mean(axis=-1),
cell.y.mean(axis=-1),
cell.z.mean(axis=-1))):
r_norm[:, i] = np.linalg.norm((r.T - np.r_[x, y, z]).T, axis=0)
V_gt = (1 / (4 * np.pi * sigma * r_norm)) @ imem
self.assertTrue(np.all(V_ex == V_gt))
def test_RecExtElectrode_04(self):
"""test RecExcElectrode implementation,
method='root_as_point' and rootinds parameter"""
cell = get_cell(n_seg=4)
sigma = 0.3
r = np.array([1, 0, 2])
# all point sources
el0 = lfp.PointSourcePotential(cell=cell,
x=np.array([r[0]]),
y=np.array([r[1]]),
z=np.array([r[2]]),
sigma=sigma)
M0 = el0.get_transformation_matrix()
# all line sources
el1 = lfp.LineSourcePotential(cell=cell,
x=np.array([r[0]]),
y=np.array([r[1]]),
z=np.array([r[2]]),
sigma=sigma)
M1 = el1.get_transformation_matrix()
# vary which index is treated as point
ids = np.arange(cell.totnsegs)
for i in range(cell.totnsegs):
el = lfp.RecExtElectrode(cell=cell,
x=r[0],
y=r[1],
z=r[2],
sigma=sigma,
method='root_as_point',
rootinds=np.array([i]))
M = el.get_transformation_matrix()
np.testing.assert_almost_equal(M0[0, i], M[0, i])
np.testing.assert_equal(M1[0, ids != i], M[0, ids != i])
# multiple roots
for i in range(cell.totnsegs - 1):
rootinds = np.array([i, i + 1])
notroots = np.ones(cell.totnsegs, dtype=bool)
notroots[rootinds] = False
el = lfp.RecExtElectrode(cell=cell,
x=r[0],
y=r[1],
z=r[2],
sigma=sigma,
method='root_as_point',
rootinds=rootinds)
M = el.get_transformation_matrix()
np.testing.assert_allclose(M0[0, rootinds], M[0, rootinds])
np.testing.assert_equal(M1[0, notroots], M[0, notroots])
def test_PointSoucePotential_01(self):
'''test PointSourcePotential implementation, when contact is within
d/2 distance to segment'''
cell = get_cell(n_seg=1)
cell.d = np.array([2.])
sigma = 0.3
r = np.array([[0.1254235242],
[0.],
[cell.z.mean()]])
psp = lfp.PointSourcePotential(cell=cell, x=r[0], y=r[1, ], z=r[2, ],
sigma=sigma)
M = psp.get_transformation_matrix()
imem = np.array([[0., 1., -1.]]) * (4 * np.pi * sigma * cell.d[0] / 2)
V_ex = M @ imem
V_gt = np.array([[0., 1., -1.]])
np.testing.assert_allclose(V_ex, V_gt)